private static ExitCodes ProgramExecution() { string cachePath = CacheConstants.TranscriptPath(_inputPrefix); var(refIndexToChromosome, _, _) = SequenceHelper.GetDictionaries(_compressedReferencePath); var cache = TranscriptCacheHelper.GetCache(cachePath, refIndexToChromosome); var geneToInternalId = InternalGenes.CreateDictionary(cache.Genes); using (var writer = new GffWriter(GZipUtilities.GetStreamWriter(_outputFileName))) { var creator = new GffCreator(writer, geneToInternalId); creator.Create(cache.TranscriptIntervalArrays); } return(ExitCodes.Success); }
private static ExitCodes ProgramExecution() { Source transcriptSource = ParseVepCacheDirectoryMain.GetSource(_transcriptSource); string cachePath = CacheConstants.TranscriptPath(_inputPrefix); IDictionary <ushort, IChromosome> refIndexToChromosome = SequenceHelper.GetDictionaries(_compressedReferencePath).refIndexToChromosome; TranscriptCacheData cache = TranscriptCacheHelper.GetCache(cachePath, refIndexToChromosome); IDictionary <IGene, int> geneToInternalId = InternalGenes.CreateDictionary(cache.Genes); using (var writer = new GffWriter(GZipUtilities.GetStreamWriter(_outputFileName))) { var creator = new GffCreator(writer, geneToInternalId, transcriptSource); creator.Create(cache.TranscriptIntervalArrays); } return(ExitCodes.Success); }